A family tree for brewer's yeast

I wrote a series of blog posts on the family tree of yeast,
starting at the very top and continuing all the
way down to the family of yeast species. The
story doesn't end there, however, because within the species of
Saccharomyces cerevisiae (ale yeast) the different strains form
a family tree of their own. However, when I wrote those blog posts in
2015 the shape of this tree was poorly understood.

That changed with the publication of a landmark paper in Cell in
2016[1], where no less than 450 yeast strains were assembled into one
big family tree. That really did give us an outline of the family
tree, and the results were fairly startling, so I want to try to share
them.

What and how

The researchers started by collecting 157 strains of yeast. All of
these belonged to the same species, Saccharomyces cerevisiae,
which is the yeast species used to ferment most beers, but not lager.
There is a family tree of strains because even though they belong to
the same species they don't all have the same genes. Think about human
beings, Homo sapiens. Hair colour, hair shape, skin colour, and
so on, all differ because of genetic differences. Some people cannot
smell acetaldehyde because they lack the necessary gene, while others
can.

Fermenting beer, Pihtla, Saaremaa, Estonia

It's the same with yeast. All strains of ale yeast are broadly
similar, but not the same. So basically, two yeast cells belong to the
same strain if they are genetically identical. Or nearly identical.

The researchers sequenced the genes of all these yeast strains.
That is, they decoded their genes, so they could read them as
sequences of one of the four molecules that code the genes, something
like this: AACTGGCA... They sequenced the entire genome, which is
about 6300 genes, but only used about a third of it, 2020 genes. They
deliberately left out the non-coding part of the genome, because (I'm
guessing) they considered that irrelevant mutations in the
non-functional part would be noise which could disturb the results.

They then used the genomes to build a family tree by looking at
which strains had the most similar set of genes to which others. The
ones that were the most similar to each other were assumed to be
closely related, and the more different ones to be more distantly
related. Using this approach they were able to have a computer
algorithm build a family tree. Then they extended the tree with 293
more strains, which they had less genetic data on, but still enough to
build a reasonable tree.

The actual tree

So, let's turn to the actual tree. Note that the researchers only
put in the genes, without telling the computer what sort of yeast they
came from. The collection contained not just beer yeast, but also wine
yeast, Asian rice wine yeasts, wild yeasts, and even yeast collected
from infected human beings. The output was:

Simplified family tree, redrawn after Gallone et al[1]

Two big groups are called "Beer 1" and "Beer 2", where "Beer 2" is
more closely related to the "Wine" group than to the first group, and
the first group is more closely related to the "Mixed" group. The
"Wild" group is the furthest away from all the others.

This suggests that most brewing yeasts fall into one of two
different groups. (There were some beer yeasts that didn't land in
either "Beer 1" or "Beer 2".) Unfortunately, the paper does not
identify the individual strains, and it says very little about the
differences between the two groups, so this is less useful than it
might sound, but it's still fascinating. Let's hope more details on
the two groups will be forthcoming with time.

From the diagrams in the paper we can deduce some differences
between the two groups:

The Beer 2 yeasts tend to have higher alcohol tolerance.

The Beer 1 yeasts are better at fermenting maltotriose.

The Beer 2 yeasts handle drying better.

However, it gets more intriguing that this, because variation
within "Beer 1" is so small that the researchers concluded that the
whole group must derive from a single ancestor that lived 3-4
centuries ago. The result for "Beer 2" is much the same. That's
startling, because it implies that nearly all of the yeasts brewers
use today descend from just two original strains of yeast back in the
1600s.

That's really bizarre. Think about how many different ale breweries
there have been over the last 3-4 centuries, all over Ireland, the UK,
France, Belgium, the Netherlands, Germany, Scandinavia, etc etc. All
of these have used one or more yeast strains that they got from some
other brewer when starting up (except the very few breweries using
spontaneous fermentation). Seemingly they have all used descendants of
the same two strains. How on earth could that happen?

I'll try to return to that in a later blog post. Meanwhile, let's
look at another fascinating insight.

Domestication

The researchers also looked at which genes actually make the
differences between these groups. Let's start with the "Wild" group.
These are yeasts that live in nature. This is where all the yeast
strains started, but some gradually moved into breweries and by now
descend from yeasts that lived there for centuries, without ever
venturing back into the wild. So how did the genes of the
"domesticated" yeasts change?

The "Wine" group shows the smallest changes from the wild.
Basically, they lost their ability to ferment maltotriose (a sugar
from malts, which doesn't exist in wine), and they became more
tolerant to the kinds of stresses yeast experience when fermenting
wine must. Other than that they don't seem to have changed that much.
They're still good at surviving in nature, for example. So, basically,
the wine yeasts are domesticated, but less so than the beer yeasts.

This makes sense, because wine is made only once per year (when the
grapes are ripe), and historically the yeast would then spend the rest
of the year in the wild, before fermenting next year's vintage. So
wine has been through fewer generations of fermenting wine, and even
spent at least some time in the wild in between.

The wine yeasts also turn out to have high tolerance for sulfites
and copper, both of which are used in wine production. The other yeast
groups have visibly less tolerance for copper and sulfites.

The beer yeasts show much bigger changes. They have become better
at fermenting maltotriose, they have lost the genes for off flavours,
they survive poorly in nature (see image above), and parts of the
genome have decayed. This is what you'd expect from an organism that
has spent thousands of generations in an environment that is far less
harsh than nature, where it is taken care of, fed, and where humans
actively select the strains they like best. Parts of the genome decay
simply because they are no longer needed. For example, the genes that
enable these yeasts to survive drying are crucial in nature and next
to useless in a brewery.

The flavour change is interesting. Two genes, PAD1
and FDC1, control the production of 4-vinyl guaiacol (4-VG), a
phenolic off-flavour. The wild yeasts generally have these, but in the
Beer 1 and 2 groups these genes have usually been destroyed by
nonsense mutations. Analysis of the tree suggests that these mutations
happened quite early in the history of these yeasts. So very likely
humans actively selected, kept, and perhaps shared the yeasts that
didn't make these flavours, and threw away the ones that did.

The way the yeasts have been shaped by how humans use them is shown
very clearly in the image above. The wine and "Asia" yeasts (sake,
rice wine, etc) have the highest alcohol tolerance, which is entirely
logical, since these are the strongest drinks.

Note that what you are looking at here is actually evolution in
practice. A combination of mutations, natural variation, natural
selection, and some human selection have combined to change living
organisms to make them better adapted to their environment, whether
that is a brewery, winery, or a sake brewery. The researchers estimate
that the changes to the beer yeasts have taken about 75,000
generations, so we're looking a time span that if translated to human
generations would be about 1,500,000 years.

History

The paper has even more to offer than this, because the researchers
tried to estimate how long ago the last common ancestors in each of
the groups Beer 1 and Beer 2 lived. Based on the rate of mutation and
some assumptions about the number of yeast generations per year, they
estimate that Beer 1 started diverging some time between 1573-1604 CE,
and Beer 2 some time 1645-1671 CE. (Note that Beer 1 and Beer 2
separated far earlier than that.) That's astonishingly recent, for
reasons that we will return to.

The researchers then looked at where the yeasts came from, and how
that fit into the tree. In Beer 1, the deepest split is between
Belgian and German yeast on one side, and British and American on the
other side. The Belgian and the German yeasts are mixed together, but
there is an American subgroup, distinct from the British.

This would seem to imply that a very large proportion of the
brewing yeasts in these countries all descend from a single strain. So
breweries somewhere in Europe must have, somehow, gotten hold of a
strain that was then shared throughout four different countries, and
that was also taken across the Atlantic to the US. You really have to
wonder how and why that happened.

I used to think that the yeasts sold as "American ale yeast" were
really European yeasts that crossed the Atlantic in the last few
decades and that considering them American was more of a marketing
ploy than strict historical fact. The results in this paper, however,
indicate that there really is a separate lineage of yeasts that have
developed in America over a substantial period of time.

Problematic history

The authors also write some things I consider unfortunate, because
in my opinion they further misunderstandings about the history of
yeast. For example, they write that "because early brewers,
winemakers, and bakers were unaware of the existence of yeast, there
is no record of how yeasts made their way into these processes." This
is not true at all. We have accounts from the 16th and 17th centuries
telling us exactly this. Also, people might not have known what yeast
was in precise biological terms, but they knew it existed, they had
words for it, equipment for using it, and they knew how to use it.

To this the researchers respond:

Yes, 16th century brewers kind of knew what yeast is, in the sense
that they learned to reclusive the sediment (mostly yeast) and had
words to describe this. But, they did likely not realize that this
material consisted of living organisms, microbes, and that they were
selecting and domesticating these organisms (in contrast to pets and
livestock). So, that is the point we wanted to make in the paper.

I agree that brewers at this time probably were not aware that
yeast was a living organism, and they definitely were not breeding it
deliberately the way they did with livestock. The interesting thing
(which is the point the authors were really making) is that brewers
effectively did breed these yeasts without knowing it.

Later, they write that the start date for Beer 1 (1573-1604)
suggests "that domestication started around this time. Interestingly,
this coincides with the gradual switch from home-centered beer brewing
where every family produced their own beer, to more professional
large-scale brewing, first in pubs and monasteries and later also in
breweries."

Site of 17th century brewery, Leuven, Belgium

However, large-scale brewing began much earlier, as William Unger
documents[2]. In the 13th century beer was a major export article and
income from taxation on it was very important for nation states and
city states. Already in the 15th century commercial brewers were using
copper kettles of 4000-5000 liters. That is definitely professional
large-scale brewing, well over a century before 1573.

The authors responded to this, too, as follows:

We would like to clarify that with large-scale brewing and industrial
breweries, we are not referring only to the appearance of relatively
big breweries (probably already present before 1500) but to the
industrialization of the brewing industry, including intensified trade
across long distances. I think it's relevant to mention this passage
in the Comprehensive history of beer brewing,
2009 by FG Meussdoerffer, p18-19:

"By the sixteenth century the infrastructure in Central Europe had
improved so far that traveling and transport became possible at speeds
not encountered since he times of the Roman legions. Thus, overland
transport became feasible, even for commodities like beer, although at
low volumes and high costs."

I think the authors make a reasonable point here, and in the end it
comes down to how big a brewery needs to be to be considered big,
which is obviously subjective. However, I believe domestication of
yeast very likely began so long before this time frame that the
discussion is moot. The evidence is a bit involved, so that will have
to be a subject for a different blog post.

And kveik?

So how does kveik and the other farmhouse
yeasts, such as the Lithuanian and the Chuvashian ones, fit into this?
Is kveik "Beer 3"? Right now, nobody has any idea at all. However,
since these very likely come out of a completely different historical
background, chances are that fitting them into the tree could tell us
a lot more about the history of yeast. So far, nobody's actually
looking at that. Unfortunately. A couple of groups of researchers are
hoping to gather the necessary funds to find out. Let's hope they
succeed.

I have a joke for you, "A historian and a microbiologist walk into a bar..."

Lars Marius Garshol - 2017-08-09 05:39:39

Hmmmmmm. I don't think I get it. :-)

Tyson - 2017-08-10 05:40:34

Should publish some links for the researchers who need funding for the next phase. I'm sure the beer community could do a lot for making it happen. I'd post it up in my small store and put at least something in. I already have the beer periodic table and a few other discussion building items up.

Excellent paper! I already knew the orginal paper - but now I understand it :-) Thank you.

A short comment on the improved logistics infrastructure in Central Europe: The celts apparently layed out the roads we now know as Roman Roads, the Romans paved it (which certainly sped up travelling). In the 8th century notable quantities of wine were transported from Italy over the Alps to the Danube. Improved transportation facilities cannot really explain the centralization of beer production in the Late Middle Ages.

Lars Marius Garshol - 2017-08-11 10:12:14

@Tyson: It doesn't seem like the researchers themselves want to work this way. Unfortunately. Otherwise I'd agree that this seems like a good way to fund it.

@Ulrich: I'm tempted to agree. Wine was exported from the Mediterranean to Scandinavia long before the birth of Christ. So it's difficult to see that anything changed very much around 1500. And even long after then most of the export of beer appears to have gone by ship.

qq - 2017-08-14 11:27:13

The kind of DNA you use for this kind of study depends on the timescale you are studying. For instance if you are studying recent changes in DNA, such as changes that have happened since humans became a species because eg police want to identify individual people ("DNA fingerprinting") then you want DNA that changes fast, because it has little selection pressure, so you use "junk" DNA. If you're looking at the deep relationships between eg vertebrates and echinoderms over 100's of millions of years then you want DNA that changes very slowly because it codes really important genes where mutations are usually fatal, things like the basic mechanism for making proteins. For this kind of study you want the genes in between, that have some selection pressure but are not fatal if they change - things like skin colour or lactose tolerance in humans.

I wouldn't take the dates too literally - all the geneticists can "see" are generations, and the dates depend heavily on what assumptions you make about how many generations the main lineage experienced per year. They seem to assume about 200 generations per year - but the main lineage will see far fewer than that if you're doing seasonal brewing (eg Märzen) or storing kveik on a ring, and in turn that will push the split further back in time.

It is intriguing to see so few families of yeast though, when yeast is a ubiquitous thing - you can always find some kind of yeast for a wild fermentation. That implies the spread of a certain beer culture that was so obviously "better" than earlier "farm" beers. The fact that this seems to have happened in the late Middle Ages suggests that the spread of domestic yeast seems to have happened alongside the big change in beer culture at that time - hops. It would be interesting to try and map where the new yeast appeared, I suspect domestic yeast and hops are very closely related in time and space.

PS Lars - I owe you thanks, we were talking at the Great British Beer Festival about Lithuanian beer, and reading your stuff meant that I didn't sound a complete idiot! :-)